3ONE

Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with adenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).

Brzezinski, K.Dauter, Z.Jaskolski, M.

(2012) Acta Crystallogr.,Sect.D 68: 218-231

  • DOI: 10.1107/S0907444911055090
  • Primary Citation of Related Structures:  
  • Also Cited By: 6EXI, 5M67, 5M66, 5M5K, 5M65, 4LVC

  • PubMed Abstract: 
  • S-Adenosyl-L-homocysteine hydrolase (SAHase) catalyzes the reversible breakdown of S-adenosyl-L-homocysteine (SAH) to adenosine and homocysteine. SAH is formed in methylation reactions that utilize S-adenosyl-L-methionine (SAM) as a methyl donor. By ...

    S-Adenosyl-L-homocysteine hydrolase (SAHase) catalyzes the reversible breakdown of S-adenosyl-L-homocysteine (SAH) to adenosine and homocysteine. SAH is formed in methylation reactions that utilize S-adenosyl-L-methionine (SAM) as a methyl donor. By removing the SAH byproduct, SAHase serves as a major regulator of SAM-dependent biological methylation reactions. Here, the first crystal structure of SAHase of plant origin, that from the legume yellow lupin (LlSAHase), is presented. Structures have been determined at high resolution for three complexes of the enzyme: those with a reaction byproduct/substrate (adenosine), with its nonoxidizable analog (cordycepin) and with a product of inhibitor cleavage (adenine). In all three cases the enzyme has a closed conformation. A sodium cation is found near the active site, coordinated by residues from a conserved loop that hinges domain movement upon reactant binding. An insertion segment that is present in all plant SAHases is located near a substrate-pocket access channel and participates in its formation. In contrast to mammalian and bacterial SAHases, the channel is open when adenosine or cordycepin is bound and is closed in the adenine complex. In contrast to SAHases from other organisms, which are active as tetramers, the plant enzyme functions as a homodimer in solution.


    Related Citations: 
    • Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.
      Reddy, M.C.,Kuppan, G.,Shetty, N.D.,Owen, J.L.,Ioerger, T.R.,Sacchettini, J.C.
      (2008) Protein Sci. 17: 2134
    • Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
      Brzezinski, K.,Bujacz, G.,Jaskolski, M.
      (2008) Acta Crystallogr.,Sect.F 64: 671
    • Bayesian phylogenetic analysis reveals two-domain topology of S-adenosylhomocysteine hydrolase protein sequences.
      Stepkowski, T.,Brzezinski, K.,Legocki, A.B.,Jaskolski, M.,Bena, G.
      (2005) MOL.PHYLOGENET.EVOL. 34: 15
    • Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus).
      Brzezinski, K.,Janowski, R.,Podkowinski, J.,Jaskolski, M.
      (2001) Acta Biochim.Pol. 48: 477
    • Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum.
      Tanaka, N.,Nakanishi, M.,Kusakabe, Y.,Shiraiwa, K.,Yabe, S.,Ito, Y.,Kitade, Y.,Nakamura, K.T.
      (2004) J.Mol.Biol. 343: 1007
    • Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
      Hu, Y.,Komoto, J.,Huang, Y.,Gomi, T.,Ogawa, H.,Takata, Y.,Fujioka, M.,Takusagawa, F.
      (1999) Biochemistry 38: 8323
    • Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.
      Turner, M.A.,Yuan, C.S.,Borchardt, R.T.,Hershfield, M.S.,Smith, G.D.,Howell, P.L.
      (1998) Nat.Struct.Mol.Biol. 5: 369


    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. kbrzezinski@anl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosylhomocysteinase
A, B
488Lupinus luteusMutation(s): 0 
Gene Names: SAHH (SHH)
EC: 3.3.1.1
Find proteins for Q9SP37 (Lupinus luteus)
Go to UniProtKB:  Q9SP37
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
ADE
Query on ADE

Download SDF File 
Download CCD File 
A, B
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 122.024α = 90.00
b = 122.024β = 90.00
c = 126.435γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references
  • Version 1.2: 2014-02-19
    Type: Database references